deepcelltypes interactive demo

Cell-type prediction for multiplexed spatial proteomic data.

To run the demo, you will need: #. Python #. A running docker daemon #. The prototype model and example data

Setup

Docker

Ensure that your docker daemon is running and doesn't require elevated permissions:

docker run hello-world

Python

Create a Python virtual environment and install the necessary dependencies:

python -m venv demo-env
source demo-env/bin/activate  # or whichever script is appropriate for your shell
pip install -r requirements.txt

Model and example data

The model is not (yet) publicly available as it is currently under development. For access to the demo data and model prototype, direct inquiries to vanvalenlab@gmail.com.

The model and data should be unpacked in the top-level directory of this repository:

tar -xzf demo_data_model.tar.gz

Running the demo

The demo is available in the form of a markdown-based jupyter notebook. Launch a new session with:

jupyter notebook

Then right-click presentation.md and select Jupytext Notebook from the Open with menu.